From 7c930f1c9222da1b076e28166128df6257a43428 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Mon, 14 Nov 2011 13:26:29 -0500
Subject: [PATCH] Tool help updates.

---
 tools/filters/secure_hash_message_digest.xml | 6 ++++++
 tools/filters/wc_gnu.xml                     | 6 ++++++
 tools/peak_calling/ccat_wrapper.xml          | 4 +++-
 tools/peak_calling/macs_wrapper.xml          | 2 ++
 4 files changed, 17 insertions(+), 1 deletion(-)

diff --git a/tools/filters/secure_hash_message_digest.xml b/tools/filters/secure_hash_message_digest.xml
index bb74edc1137..e20ce80969a 100644
--- a/tools/filters/secure_hash_message_digest.xml
+++ b/tools/filters/secure_hash_message_digest.xml
@@ -35,5 +35,11 @@
 
 This tool outputs Secure Hashes / Message Digests of a dataset using the user selected algorithms.
 
+------
+
+**Citation**
+
+If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
+
     </help>
 </tool>
diff --git a/tools/filters/wc_gnu.xml b/tools/filters/wc_gnu.xml
index 5d3ad1e3565..9138fef505c 100644
--- a/tools/filters/wc_gnu.xml
+++ b/tools/filters/wc_gnu.xml
@@ -62,5 +62,11 @@ This tool outputs counts of specified attributes (lines, words, characters) of a
   #lines  words  characters
   7499	  41376	 624971
 
+------
+
+**Citation**
+
+If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
+
     </help>
 </tool>
diff --git a/tools/peak_calling/ccat_wrapper.xml b/tools/peak_calling/ccat_wrapper.xml
index 47a107586be..76cc93cbeee 100644
--- a/tools/peak_calling/ccat_wrapper.xml
+++ b/tools/peak_calling/ccat_wrapper.xml
@@ -112,7 +112,7 @@ bootstrapPass	${options_type[ 'bootstrap_pass' ]}
       <output name="output_top_file" file="peakcalling_ccat/3.0/ccat_test_top_out_1.interval.sorted.re_match" compare="re_match" sort="true" />
       <output name="output_log_file" file="peakcalling_ccat/3.0/ccat_test_log_out_1.txt" />
     </test>
-    <!-- Test below gives different results on different architectures, 
+    <!-- Test below gives different answers on different architectures, 
     e.g.: x86_64 GNU/Linux gave an extra line (additional peak called) when compared to the version running on 10.6.0 Darwin i386 
     slidingWinSize was fixed to be 1000, default as per readme.txt
     -->
@@ -140,6 +140,8 @@ View the original CCAT documentation: http://cmb.gis.a-star.edu.sg/ChIPSeq/paper
 
 **Citation**
 
+For the underlying tool, please cite `Xu H, Handoko L, Wei X, Ye C, Sheng J, Wei CL, Lin F, Sung WK. A signal-noise model for significance analysis of ChIP-seq with negative control. Bioinformatics. 2010 May 1;26(9):1199-204. &lt;http://www.ncbi.nlm.nih.gov/pubmed/20371496&gt;`_
+
 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
 
   </help>
diff --git a/tools/peak_calling/macs_wrapper.xml b/tools/peak_calling/macs_wrapper.xml
index a32c801a6bc..6601102b306 100644
--- a/tools/peak_calling/macs_wrapper.xml
+++ b/tools/peak_calling/macs_wrapper.xml
@@ -231,6 +231,8 @@ View the original MACS documentation: http://liulab.dfci.harvard.edu/MACS/00READ
 
 **Citation**
 
+For the underlying tool, please cite `Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137. &lt;http://www.ncbi.nlm.nih.gov/pubmed/18798982&gt;`_
+
 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
 
   </help>